The Mesosphere and Lower Thermosphere (MLT) region of the atmosphere to be studied by TIMED is located between 60–180 km above the Earth's surface where energy from solar radiation is first deposited into the atmosphere. This can have profound effects on Earth's upper atmospheric regions, particularly during the peak of the Sun's 11-year solar cycle when the greatest amounts of its energy are being released. Understanding these interactions is also important for our understanding of various subjects in geophysics, meteorology, and atmospheric science, as solar radiation is one of the primary driving forces behind atmospheric tides. Changes in the MLT can also affect modern satellite and radiotelecommunications.

The spacecraft payload consists of the following four main instruments:

Global Ultraviolet Imager (GUVI): A spatial-scanning, far-ultraviolet spectrograph designed to globally measure the composition and temperature profiles of the MLT region, as well as its auroral energy inputs.

Solar Extreme Ultraviolet Experiment (SEE): A spectrometer and a suite of photometers designed to measure the solar soft X-rays, extreme-ultraviolet and far-ultraviolet radiation that is deposited into the MLT region.

TIMED Doppler Interferometer (TIDI): Designed to globally measure the wind and temperature profiles of the MLT region.

Sounding of the Atmosphere using Broadband Emission Radiometry (SABER): Multichannel radiometer designed to measure heat emitted by the atmosphere over a broad altitude and spectral range, as well as global temperature profiles and sources of atmospheric cooling.